This sequencing was carried out to compare methodologies for de novo assembly of Anopheles mosquito genomes from Illumina reads. A single individual mosquito, from the An. gambiae Pimperena S colony (molecular form S), was used to generate small-insert (180 bp, 3 kb) libraries. A pool of individuals from the same colony was used to generate a library with fosmid-scale (38 kb) inserts. Reads were assembled using the ALLPATHS LG program.